Comparative Genomics Strategy
Comparative Genomics utilizes bioinformatic approaches for making inferences about biology or evolution from a comparison of genome sequence data from different species. Depending on the depth of divergence of the taxa being compared, it is possible to infer recent or deep evolutionary patterns, or to infer protein function.
At one extreme, a comparison of genome sequences of species that occur across the tree of life (archaea, eubacteria, and eukarya) might provide data that suggests a "core" set of genes required for all life (for example, read Minimal Gene Sets (Acrobat (PDF) 299kB Oct16 09). To look broadly at evolution of genomes, you can browse a database that catalogs all the genome projects that are currently underway (Genomes Online Database (GOLD)).
Understanding the evolution of animal genes and genomes can be approached by comparing genes/genomes of animals at different levels of divergence in the animal lineage, for example choanoflagellates as an example of a "pre-animal" animal-like cell, sponges as a non-tissue grade collection of interacting animal-like cells, cnidarians as simple tissue-level animals, and humans as organ systems-level complexity.
To help you think about the types of questions that you could ask, you could consider a question that can only be addressed using genomic methods: how does morphological complesity of animals relate to genomic complexity?
As background, consider the placement of cnidarians in the animal phylogeny, as an early branching lineage. It is morphologically simple. Therefore it seems intuitive to assume that cnidarians must have a simpler genome than more morphologically complex animals, such as humans. But comparative genomics studies have now shown that "simple" animals, such as cnidarians, possess as complex a gene repertoire as the "higher" animals.
A Sea Anemone Genome Reveals Ancestral Eumatazoan Gene Repertoire (Putnam et. al. 2007) (Acrobat (PDF) 372kB Nov5 09).
Some things you might consider doing are using genomes of other species as a way to better characterize Aiptasiagenes, or identify orthologs in Aiptasia and other animals to do a phylogenetic study. For the purposes of doing comparative genomic studies, it is useful to have access to genome sequences of many different species. One of the predominant genome centers that has focused on sampling across the Tree of Life, is the Joint Genome Institute. The JGI houses databases and Genome Browsers for species ranging from Archaea to Human.
Portal to all JGI Genome Projects and Genome Browsers
For the purposes of doing comparative genomics with cnidarians as a focus, you might be particularly interested in investigating the genomes Nematostella(sea anemones) and Monosiga brevicollis.
Nematostella can be valuable as a way to get more complete information about the potential structure and function of genes of interest for which you might have only incomplete sequence information from Aiptasia.
To look at bit farther back, you might be interested in comparisons to the genome of the choanoflagellate Monosiga brevicollis,a unicellular eukaryote that appears to be the closest living relative to the animal phylum.